Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtcttatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC

Basic information

species Oryza sativa
transcript LOC_Os09g39462.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G066939_T01 (Zea mays), 3'ss of exon 1
-tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtct-tatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
  |   ||  || ||  || |  | | |||   |   |  |  ||    |   | | | || | ||  ||||||  | ||  |||||| |  ||   || ||||||||| ||||||||||| |||||||||||||||||||||||||  |  ||||||| ||| ||| |||| ||||| ||||| || ||||||||||||||
ggaactttacattttactgttccattgcctaa-tgctttaatattaatcgacaaaatacgcctagtc-cttgtatttgactccagtctattcctttctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTCATGACCCTAGTCGTACAGAGTATGAATTCAATGGCCTTCCAACTTCGTATCTGCGTCTTGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G103345_T01 (Zea mays), 3'ss of exon 1
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtct-tatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
 |   ||  || || |   ||   |  | |  |   |  |  ||    |   | | | || | ||  ||||||  | ||  |||||| |  ||   || ||||||||| ||||||||||| |||||||||||||||||||||||||  |  ||||||| ||| ||| |||| ||||| ||||| || ||||||||||||||
gaactttacattttgactgttccattgcctaatgctttaatattaatcgacaaaatacgcctagtc-cttgtatttgaccccagtctattcctttctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTCATGACCCTAGTCGTACAGAGTATGAATTCAATGGCCTTCCAACTTCGTATCTGCGTCTTGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G030259_T01 (Zea mays), 3'ss of exon 1
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtct-tatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
 |   ||  || || |   ||   |  | |  |   |  |  ||    | | | | | || | ||  ||||||  | ||  |||||| |  ||  ||| ||||||||| ||||||||||| |||||||||||||||||||||||||  |  ||||||| ||| ||| |||| ||||| ||||| || ||||||||||||||
gaactttacattttgactgttccattgcctaatgctttaatattaatcgataaaatacgcctagtc-cttgtatttgactccagtctattcctttttgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTCATGACCCTAGTCGTACAGAGTATGAATTCAATGGCCTTCCAACTTCGTATCTGCGTCTTGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009575_T01 (Zea mays), 3'ss of exon 2
tactgttgtatcttcatgattgactacct-ttctaactacaagttgtaagttgagaaatgcttcgtgg-----cttgtaccttacagcagtcttatctcat-tgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
         ||  | | |    | |   | ||| ||  ||    || |   |||     |  | || |     ||||||  | ||   |||||  ||   | || ||||||||| ||||||||||| |||||||||||||||  |||||||| |   ||||||| ||| ||| |||||||||| ||||| ||  ||||||| |||||
------aaaattatgaagtgcaagtttttgttccaagcaccttatgcat-ctgatggtcgtgtggtcggagtccttgtatttgactctagtctattcctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTACAGAGTATGAATTCAATGGTCTTCCAACTTCATATTTGCGTCTCGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G054998_T01 (Zea mays), 3'ss of exon 1
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggc-ttgtaccttacagcagtct-tatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
 |   ||  || || |   ||  | |       |      | |  |||    | |||| |  |  | | |||||  | ||  |||||| |  ||   || ||||||||| ||||||||||| |||||||||||||||||||||||||  |  ||||||| ||| ||| |||| ||||| ||||| || ||||||||||||||
gaactttacattttgactgtt--ccattgcctaatgctttaatattaatcgaaaaaatacggccagtccttgtatttgactccagtctattcctttctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTCATGACCCTAGTCGTACAGAGTATGAATTCAATGGCCTTCCAACTTCGTATCTGCGTCTTGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009624_T02 (Zea mays), 3'ss of exon 1
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtct-tatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
 |   ||  || || |   ||   |  | |  |   |  |  ||    |   | | | || | ||  ||||||  | ||  |||||| |  ||  ||| ||||||||| ||||||||||| |||||||||||||||||||||||||  |  ||||||| ||| ||| |||| ||||| ||||| || ||||||||||||||
gaactttacattttgactgttccattgcctaatgctttaatattaatcgacaaaatacgcctagtc-cttgtatttgactccagtctattcctttttgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTCATGACCCTAGTCGTACAGAGTATGAATTCGATGGCCTTCCAACTTCGTATCTGCGTCTTGCTGC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 1
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtcttatctcattgt----agTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
     ||  |     ||   ||  ||   || |||        |||   |||       | |      |  ||      |  | |  ||    ||| |    ||| ||||||||||||||||||||   ||||||||||||||| ||||| ||     |  | || || ||     | ||||| || || || ||  | |||||
----atttaaatgcgatacatgtgtaagattgtaatatttgagtgtgtattgctgttatcctttctattcatataactaaagatttataatctattttgttcagTTCTAAGGATGGAGCAAGACATCGAGAAGTTCATTCATGATCCTACTCAACAGCAACTAGAGTTTCAACAGTTGCCTACCTCCTATCTACGGTTGGCTGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88345685|gb|CI630953.1|CI630953
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCCAG
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGC-AG
EST: gi|88299149|gb|CI570119.1|CI570119
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAACGTTCATTCATGACCCTACGCAG
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAA-GTTCATTCATGACCCTACGCAG
EST: gi|88311449|gb|CI572505.1|CI572505
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGAC
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGAC
EST: gi|29633027|gb|CB638036.1|CB638036
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
EST: gi|3762486|gb|C99734.1|C99734
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTTACGCAG
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCT-ACGCAG
EST: gi|88449673|gb|CI565651.1|CI565651
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
EST: gi|117236321|gb|CT842251.1|CT842251
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCGGA
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
EST: gi|29630436|gb|CB635445.1|CB635445
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCGGA
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGA
EST: gi|88318141|gb|CI629422.1|CI629422
EST:     CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTG                         TGCTAAGGATGGAGCA
genomic: CGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatatt ... ctcattgtagTGCTAAGGATGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttgagaaatgcttcgtggcttgtaccttacagcagtcttatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC
                           accttac  putative branch site (score: 3)
                                       tcttatctc  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgttgtatcttcatgattgactacctttctaactacaagttgtaagttgagaaatgcttcgtggcttgtaccttacagcagtcttatctcattgtagTGCTAAGGATGGAGCAAGACATTTTGAAGTTCATTCATGACCCTACGCAGACAGAGTTTGACTTCCATGGTCTTCCTACTTCTTACCTGCGTCTTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC